//Created by libAntimony v2.4
model bagci_2006__environment(time_)

  // Variable initializations:
  time_ = ;
end

model bagci_2006__Casp8(Casp8, Casp8Bid, Bid, J_0, J_f0, k_f0, k_10, k_00, u, time_)

  // Assignment Rules:
  J_0 := k_10 * Casp8 * Bid - k_00 * Casp8Bid;
  J_f0 := k_f0 * Casp8Bid;
  J_Casp8 := - u * Casp8;

  // Rate Rules:
  Casp8' = - J_0 + J_f0 + J_Casp8;
  Casp8Bid' = J_0 - J_f0;

  // Variable initializations:
  Casp8 = 0;
  Casp8Bid = 0;
  Bid = ;
  k_f0 = ;
  k_10 = ;
  k_00 = ;
  u = ;
  time_ = ;
end

model bagci_2006__Apaf_1(Apaf_1, CytcApaf_1, Cytc, J_1, P_Apaf_1, u, k_11, k_01, time_)

  // Assignment Rules:
  J_Apaf_1 := P_Apaf_1 - u * Apaf_1;
  J_1 := k_11 * Cytc * Apaf_1 - k_01 * CytcApaf_1;

  // Rate Rules:
  Apaf_1' = - J_1 + J_Apaf_1;

  // Variable initializations:
  Apaf_1 = 0.004;
  CytcApaf_1 = ;
  Cytc = ;
  P_Apaf_1 = ;
  u = ;
  k_11 = ;
  k_01 = ;
  time_ = ;
end

model bagci_2006__CytcApaf_1(CytcApaf_1, Apop, J_1, J_1b, k_11b, k_01b, p, time_)

  // Assignment Rules:
  J_1b := k_11b * power(CytcApaf_1, p) - k_01b * Apop;

  // Rate Rules:
  CytcApaf_1' = J_1 - 7 * J_1b;

  // Variable initializations:
  CytcApaf_1 = 0;
  Apop = ;
  J_1 = ;
  k_11b = ;
  k_01b = ;
  p = ;
  time_ = ;
end

model bagci_2006__Cytc(Cytc, J_14, J_1, u, time_)

  // Assignment Rules:
  J_Cytc := - u * Cytc;

  // Rate Rules:
  Cytc' = (J_14 - J_1) + J_Cytc;

  // Variable initializations:
  Cytc = 0;
  J_14 = ;
  J_1 = ;
  u = ;
  time_ = ;
end

model bagci_2006__Cytc_mito(Cytc_mito, Bax_2, J_14, P_Cytc_mito, k14, u, time_)

  // Assignment Rules:
  J_14 := k14 * Bax_2 * Cytc_mito;
  J_Cytc_mito := P_Cytc_mito - u * Cytc_mito;

  // Rate Rules:
  Cytc_mito' = - J_14 + J_Cytc_mito;

  // Variable initializations:
  Cytc_mito = 0.004;
  Bax_2 = ;
  P_Cytc_mito = ;
  k14 = ;
  u = ;
  time_ = ;
end

model bagci_2006__Bax_2(Bax_2, J_12b, u, time_)

  // Assignment Rules:
  J_Bax_2 := - u * Bax_2;

  // Rate Rules:
  Bax_2' = J_12b + J_Bax_2;

  // Variable initializations:
  Bax_2 = 0;
  J_12b = ;
  u = ;
  time_ = ;
end

model bagci_2006__tBid_mito(tBid_mito, Bax, J_11, J_12a, u, k12a, time_)

  // Assignment Rules:
  J_12a := k12a * tBid_mito * Bax;
  J_tBid_mito := - u * tBid_mito;

  // Rate Rules:
  tBid_mito' = (J_11 - J_12a) + J_tBid_mito;

  // Variable initializations:
  tBid_mito = 0;
  Bax = ;
  J_11 = ;
  u = ;
  k12a = ;
  time_ = ;
end

model bagci_2006__tBid(tBid, J_f0, J_f8, J_12b, J_11, u, k11, time_)

  // Assignment Rules:
  J_11 := k11 * tBid;
  J_tBid := - u * tBid;

  // Rate Rules:
  tBid' = ((J_f0 + J_f8) - J_11) + J_12b + J_tBid;

  // Variable initializations:
  tBid = 0;
  J_f0 = ;
  J_f8 = ;
  J_12b = ;
  u = ;
  k11 = ;
  time_ = ;
end

model bagci_2006__tBidBax(tBidBax, Bax, J_12a, J_12b, k12b, u, time_)

  // Assignment Rules:
  J_12b := k12b * tBidBax * Bax;
  J_tBidBax := - u * tBidBax;

  // Rate Rules:
  tBidBax' = (J_12a - J_12b) + J_tBidBax;

  // Variable initializations:
  tBidBax = 0;
  Bax = ;
  J_12a = ;
  k12b = ;
  u = ;
  time_ = ;
end

model bagci_2006__Bax(Bax, Bcl_2, J_12a, J_12b, J_13, k13, P_oBax, p53, p53_thresh, u_Bax, time_)

  // Assignment Rules:
  J_13 := k13 * Bcl_2 * Bax;
  J_Bax := P_Bax - u_Bax * Bax;
  P_Bax := P_oBax * (1 + power(p53, 4) / (power(p53, 4) + power(p53_thresh, 4)));

  // Rate Rules:
  Bax' = ((- J_12a - J_12b) - J_13) + J_Bax;

  // Variable initializations:
  Bax = 0.004;
  Bcl_2 = ;
  J_12a = ;
  J_12b = ;
  k13 = ;
  P_oBax = ;
  p53 = ;
  p53_thresh = ;
  u_Bax = ;
  time_ = ;
end

model bagci_2006__Bcl_2(Bcl_2, Casp3, Casp3Bcl_2, J_9, J_13, k_19, k_09, P_oBcl_2, u_Bcl_2, p53_thresh, p53, time_)

  // Assignment Rules:
  J_9 := k_19 * Casp3 * Bcl_2 - k_09 * Casp3Bcl_2;
  J_Bcl_2 := P_Bcl_2 - u_Bcl_2 * Bcl_2;
  P_Bcl_2 := (P_oBcl_2 * power(p53_thresh, 4)) / (power(p53, 4) + power(p53_thresh, 4));

  // Rate Rules:
  Bcl_2' = (- J_9 - J_13) + J_Bcl_2;

  // Variable initializations:
  Bcl_2 = 0.004;
  Casp3 = ;
  Casp3Bcl_2 = ;
  J_13 = ;
  k_19 = ;
  k_09 = ;
  P_oBcl_2 = ;
  u_Bcl_2 = ;
  p53_thresh = ;
  p53 = ;
  time_ = ;
end

model bagci_2006__Casp3Bcl_2(Casp3Bcl_2, J_9, J_f9, k_f9, time_)

  // Assignment Rules:
  J_f9 := k_f9 * Casp3Bcl_2;

  // Rate Rules:
  Casp3Bcl_2' = J_9 - J_f9;

  // Variable initializations:
  Casp3Bcl_2 = 0;
  J_9 = ;
  k_f9 = ;
  time_ = ;
end

model bagci_2006__Casp3Bid(Casp3Bid, Casp3, Bid, J_8, J_f8, k_18, k_08, k_f8, time_)

  // Assignment Rules:
  J_8 := k_18 * Casp3 * Bid - k_08 * Casp3Bid;
  J_f8 := k_f8 * Casp3Bid;

  // Rate Rules:
  Casp3Bid' = J_8 - J_f8;

  // Variable initializations:
  Casp3Bid = 0;
  Casp3 = ;
  Bid = ;
  k_18 = ;
  k_08 = ;
  k_f8 = ;
  time_ = ;
end

model bagci_2006__Bid(Bid, J_0, J_8, P_Bid, u, time_)

  // Assignment Rules:
  J_Bid := P_Bid - u * Bid;

  // Rate Rules:
  Bid' = (- J_0 - J_8) + J_Bid;

  // Variable initializations:
  Bid = 0.004;
  J_0 = ;
  J_8 = ;
  P_Bid = ;
  u = ;
  time_ = ;
end

model bagci_2006__Casp3(Casp3, IAP, Casp3IAP, J_f6, J_f6b, J_7, J_8, J_f8, J_9, J_f9, u, k_17, k_07, time_)

  // Assignment Rules:
  J_7 := k_17 * Casp3 * IAP - k_07 * Casp3IAP;
  J_Casp3 := - u * Casp3;

  // Rate Rules:
  Casp3' = (((((J_f6 + J_f6b) - J_7) - J_8) + J_f8) - J_9) + J_f9 + J_Casp3;
  Casp3IAP' = J_7;

  // Variable initializations:
  Casp3 = 0;
  IAP = ;
  Casp3IAP = 0;
  J_f6 = ;
  J_f6b = ;
  J_8 = ;
  J_f8 = ;
  J_9 = ;
  J_f9 = ;
  u = ;
  k_17 = ;
  k_07 = ;
  time_ = ;
end

model bagci_2006__Apop(Apop, J_1b, J_2, J_4b, time_)

  // Rate Rules:
  Apop' = (J_1b - J_2) + J_4b;

  // Variable initializations:
  Apop = 0;
  J_1b = ;
  J_2 = ;
  J_4b = ;
  time_ = ;
end

model bagci_2006__Pro9(Pro9, ApopPro9, ApopPro9_2, Apop, J_2, J_3, k_12, k_02, k_13, k_03, u, P_Pro9, time_)

  // Assignment Rules:
  J_2 := k_12 * Apop * Pro9 - k_02 * ApopPro9;
  J_3 := k_13 * ApopPro9 * Pro9 - k_03 * ApopPro9_2;
  J_Pro9 := P_Pro9 - u * Pro9;

  // Rate Rules:
  Pro9' = (- J_2 - J_3) + J_Pro9;
  ApopPro9' = J_2 - J_3;

  // Variable initializations:
  Pro9 = 0.004;
  ApopPro9 = 0;
  ApopPro9_2 = ;
  Apop = ;
  k_12 = ;
  k_02 = ;
  k_13 = ;
  k_03 = ;
  u = ;
  P_Pro9 = ;
  time_ = ;
end

model bagci_2006__ApopPro9_2(ApopPro9_2, J_3, J_f3, k_f3, time_)

  // Assignment Rules:
  J_f3 := k_f3 * ApopPro9_2;

  // Rate Rules:
  ApopPro9_2' = J_3 - J_f3;

  // Variable initializations:
  ApopPro9_2 = 0;
  J_3 = ;
  k_f3 = ;
  time_ = ;
end

model bagci_2006__ApopCasp9_2Pro3(ApopCasp9_2Pro3, ApopCasp9_2, Pro3, J_6b, J_f6b, k_16b, k_06b, k_f6b, time_)

  // Assignment Rules:
  J_6b := k_16b * ApopCasp9_2 * Pro3 - k_06b * ApopCasp9_2Pro3;
  J_f6b := k_f6b * ApopCasp9_2Pro3;

  // Rate Rules:
  ApopCasp9_2Pro3' = J_6b - J_f6b;

  // Variable initializations:
  ApopCasp9_2Pro3 = 0;
  ApopCasp9_2 = ;
  Pro3 = ;
  k_16b = ;
  k_06b = ;
  k_f6b = ;
  time_ = ;
end

model bagci_2006__Casp9Pro3(Casp9Pro3, J_6, J_f6, k_f6, time_)

  // Assignment Rules:
  J_f6 := k_f6 * Casp9Pro3;

  // Rate Rules:
  Casp9Pro3' = J_6 - J_f6;

  // Variable initializations:
  Casp9Pro3 = 0;
  J_6 = ;
  k_f6 = ;
  time_ = ;
end

model bagci_2006__Pro3(Pro3, Casp9, Casp9Pro3, J_6, J_6b, k_16, k_06, P_Pro3, u, time_)

  // Assignment Rules:
  J_6 := k_16 * Casp9 * Pro3 - k_06 * Casp9Pro3;
  J_Pro3 := P_Pro3 - u * Pro3;

  // Rate Rules:
  Pro3' = (- J_6 - J_6b) + J_Pro3;

  // Variable initializations:
  Pro3 = 0.004;
  Casp9 = ;
  Casp9Pro3 = ;
  J_6b = ;
  k_16 = ;
  k_06 = ;
  P_Pro3 = ;
  u = ;
  time_ = ;
end

model bagci_2006__IAP(IAP, Casp9IAP, ApopCasp9IAP, ApopCasp9_2IAP, ApopCasp9_2, Casp9, ApopCasp9, J_5, J_5b, J_5c, J_7, P_IAP, k_15, k_05, k_15b, k_05b, k_15c, k_05c, u, time_)

  // Assignment Rules:
  J_5 := k_15 * Casp9 * IAP - k_05 * Casp9IAP;
  J_5b := k_15b * ApopCasp9 * IAP - k_05b * ApopCasp9IAP;
  J_5c := k_15c * ApopCasp9_2 * IAP - k_05c * ApopCasp9_2IAP;
  J_IAP := P_IAP - u * IAP;

  // Rate Rules:
  IAP' = (((- J_5 - J_5b) - J_5c) - J_7) + J_IAP;
  Casp9IAP' = J_5;
  ApopCasp9IAP' = J_5b;
  ApopCasp9_2IAP' = J_5c;

  // Variable initializations:
  IAP = 0.004;
  Casp9IAP = 0;
  ApopCasp9IAP = 0;
  ApopCasp9_2IAP = 0;
  ApopCasp9_2 = ;
  Casp9 = ;
  ApopCasp9 = ;
  J_7 = ;
  P_IAP = ;
  k_15 = ;
  k_05 = ;
  k_15b = ;
  k_05b = ;
  k_15c = ;
  k_05c = ;
  u = ;
  time_ = ;
end

model bagci_2006__ApopCasp9(ApopCasp9, ApopCasp9_2, Apop, Casp9, J_4, J_4b, J_5b, k_14, k_04, k_14b, k_04b, time_)

  // Assignment Rules:
  J_4 := k_14 * ApopCasp9_2 - k_04 * ApopCasp9 * Casp9;
  J_4b := k_14b * ApopCasp9 - k_04b * Apop * Casp9;

  // Rate Rules:
  ApopCasp9' = (J_4 - J_4b) - J_5b;

  // Variable initializations:
  ApopCasp9 = 0;
  ApopCasp9_2 = ;
  Apop = ;
  Casp9 = ;
  J_5b = ;
  k_14 = ;
  k_04 = ;
  k_14b = ;
  k_04b = ;
  time_ = ;
end

model bagci_2006__Casp9(Casp9, J_4, J_4b, J_5, J_6, J_f6, u, time_)

  // Assignment Rules:
  J_Casp9 := - u * Casp9;

  // Rate Rules:
  Casp9' = (((J_4 + J_4b) - J_5) - J_6) + J_f6 + J_Casp9;

  // Variable initializations:
  Casp9 = 0;
  J_4 = ;
  J_4b = ;
  J_5 = ;
  J_6 = ;
  J_f6 = ;
  u = ;
  time_ = ;
end

model bagci_2006__ApopCasp9_2(ApopCasp9_2, J_f3, J_4, J_5c, J_6b, J_f6b, time_)

  // Rate Rules:
  ApopCasp9_2' = (((J_f3 - J_4) - J_5c) - J_6b) + J_f6b;

  // Variable initializations:
  ApopCasp9_2 = 0;
  J_f3 = ;
  J_4 = ;
  J_5c = ;
  J_6b = ;
  J_f6b = ;
  time_ = ;
end

model bagci_2006__model_constant(k_10, k_f0, k_01, k_01b, k_02, k_03, k_14, k_14b, k_15, k_15b, k_15c, k_16, k_f6, k_06b, k_17, k_18, k_f8, k_09, k11, k12b, k14, k_00, k_11, k_11b, k_12, k_13, k_f3, k_04, k_04b, k_05, k_05b, k_05c, k_06, k_16b, k_f6b, k_07, k_08, k_19, k_f9, k12a, k13, p53_thresh, u, u_Bax, u_Bcl_2, P_Apaf_1, P_IAP, P_Pro3, P_Pro9, P_Bid, P_oBcl_2, P_oBax, P_Cytc_mito, p53, p)

  // Variable initializations:
  k_10 = 10;
  k_f0 = 0.1;
  k_01 = 0.5;
  k_01b = 0.5;
  k_02 = 0.5;
  k_03 = 0.5;
  k_14 = 5;
  k_14b = 5;
  k_15 = 5;
  k_15b = 5;
  k_15c = 5;
  k_16 = 10;
  k_f6 = 0.001;
  k_06b = 0.5;
  k_17 = 5;
  k_18 = 10;
  k_f8 = 0.1;
  k_09 = 0.5;
  k11 = 10;
  k12b = 10;
  k14 = 10;
  k_00 = 0.5;
  k_11 = 5;
  k_11b = 50000;
  k_12 = 10;
  k_13 = 10;
  k_f3 = 0.1;
  k_04 = 0.5;
  k_04b = 0.5;
  k_05 = 0.0035;
  k_05b = 0.0035;
  k_05c = 0.0035;
  k_06 = 0.5;
  k_16b = 10;
  k_f6b = 0.1;
  k_07 = 0.0035;
  k_08 = 0.5;
  k_19 = 10;
  k_f9 = 0.1;
  k12a = 10;
  k13 = 10;
  p53_thresh = 0.004;
  u = 0.006;
  u_Bax = 0.006;
  u_Bcl_2 = 0.006;
  P_Apaf_1 = 0.0003;
  P_IAP = 0.00003;
  P_Pro3 = 0.0003;
  P_Pro9 = 0.0003;
  P_Bid = 0.00003;
  P_oBcl_2 = 0.00008;
  P_oBax = 0.00003;
  P_Cytc_mito = 0.0003;
  p53 = 0.0066;
  p = 4;
end

model *bagci_2006____main()

  // Sub-modules, and any changes to those submodules:
  environment: bagci_2006__environment(time_);
  Casp8: bagci_2006__Casp8(Casp80, Casp8Bid, Bid0, J_0, J_f0, k_f0, k_10, k_00, u, time_);
  Apaf_1: bagci_2006__Apaf_1(Apaf_10, CytcApaf_10, Cytc0, J_1, P_Apaf_1, u, k_11, k_01, time_);
  CytcApaf_1: bagci_2006__CytcApaf_1(CytcApaf_10, Apop0, J_1, J_1b, k_11b, k_01b, p, time_);
  Cytc: bagci_2006__Cytc(Cytc0, J_14, J_1, u, time_);
  Cytc_mito: bagci_2006__Cytc_mito(Cytc_mito0, Bax_20, J_14, P_Cytc_mito, k14, u, time_);
  Bax_2: bagci_2006__Bax_2(Bax_20, J_12b, u, time_);
  tBid_mito: bagci_2006__tBid_mito(tBid_mito0, Bax0, J_11, J_12a, u, k12a, time_);
  tBid: bagci_2006__tBid(tBid0, J_f0, J_f8, J_12b, J_11, u, k11, time_);
  tBidBax: bagci_2006__tBidBax(tBidBax0, Bax0, J_12a, J_12b, k12b, u, time_);
  Bax: bagci_2006__Bax(Bax0, Bcl_20, J_12a, J_12b, J_13, k13, P_oBax, p53, p53_thresh, u_Bax, time_);
  Bcl_2: bagci_2006__Bcl_2(Bcl_20, Casp30, Casp3Bcl_20, J_9, J_13, k_19, k_09, P_oBcl_2, u_Bcl_2, p53_thresh, p53, time_);
  Casp3Bcl_2: bagci_2006__Casp3Bcl_2(Casp3Bcl_20, J_9, J_f9, k_f9, time_);
  Casp3Bid: bagci_2006__Casp3Bid(Casp3Bid0, Casp30, Bid0, J_8, J_f8, k_18, k_08, k_f8, time_);
  Bid: bagci_2006__Bid(Bid0, J_0, J_8, P_Bid, u, time_);
  Casp3: bagci_2006__Casp3(Casp30, IAP0, Casp3IAP, J_f6, J_f6b, J_7, J_8, J_f8, J_9, J_f9, u, k_17, k_07, time_);
  Apop: bagci_2006__Apop(Apop0, J_1b, J_2, J_4b, time_);
  Pro9: bagci_2006__Pro9(Pro90, ApopPro9, ApopPro9_20, Apop0, J_2, J_3, k_12, k_02, k_13, k_03, u, P_Pro9, time_);
  ApopPro9_2: bagci_2006__ApopPro9_2(ApopPro9_20, J_3, J_f3, k_f3, time_);
  ApopCasp9_2Pro3: bagci_2006__ApopCasp9_2Pro3(ApopCasp9_2Pro30, ApopCasp9_20, Pro30, J_6b, J_f6b, k_16b, k_06b, k_f6b, time_);
  Casp9Pro3: bagci_2006__Casp9Pro3(Casp9Pro30, J_6, J_f6, k_f6, time_);
  Pro3: bagci_2006__Pro3(Pro30, Casp90, Casp9Pro30, J_6, J_6b, k_16, k_06, P_Pro3, u, time_);
  IAP: bagci_2006__IAP(IAP0, Casp9IAP, ApopCasp9IAP, ApopCasp9_2IAP, ApopCasp9_20, Casp90, ApopCasp90, J_5, J_5b, J_5c, J_7, P_IAP, k_15, k_05, k_15b, k_05b, k_15c, k_05c, u, time_);
  ApopCasp9: bagci_2006__ApopCasp9(ApopCasp90, ApopCasp9_20, Apop0, Casp90, J_4, J_4b, J_5b, k_14, k_04, k_14b, k_04b, time_);
  Casp9: bagci_2006__Casp9(Casp90, J_4, J_4b, J_5, J_6, J_f6, u, time_);
  ApopCasp9_2: bagci_2006__ApopCasp9_2(ApopCasp9_20, J_f3, J_4, J_5c, J_6b, J_f6b, time_);
  model_constant: bagci_2006__model_constant(k_10, k_f0, k_01, k_01b, k_02, k_03, k_14, k_14b, k_15, k_15b, k_15c, k_16, k_f6, k_06b, k_17, k_18, k_f8, k_09, k11, k12b, k14, k_00, k_11, k_11b, k_12, k_13, k_f3, k_04, k_04b, k_05, k_05b, k_05c, k_06, k_16b, k_f6b, k_07, k_08, k_19, k_f9, k12a, k13, p53_thresh, u, u_Bax, u_Bcl_2, P_Apaf_1, P_IAP, P_Pro3, P_Pro9, P_Bid, P_oBcl_2, P_oBax, P_Cytc_mito, p53, p);
end